To reproduce. create the following file, open in your web browser, note the results, then refresh, 2nd and subsequent runs will produce the wrong result:-

This is with php 5.3.1 and 5.3.2 and the nts version of phpexpress (3.0.1) on Ubuntu.

Have had to remove phpexpress from out configs and quickly ship unencoded code, not good!

On another point, I wonder whether a better way forward for phpexpress would be to develop and donate to the APC project a plugin architecture to allow encoders to hook into that, that way there need be no development on the caching side, we'd just use APC and when APC becomes part of the mainline php code it will already be supported?
Nusphere would then just need to maintain their plugin.

Tried under Linux and the problem wasn't reproduced (and I hardly believe it would). The results are always the same - the code executed from cache or from disk produces the same output.

Looks like something wrong is with glibc/libc on your OS. Did you check for updates?
Also, I have to say that php 5.3 in range from 5.3.0 upto 5.3.2 aren't really good and I would highly recommend to avoid them.
If you can reproduce the problem under newer versions, please submit your report to http://www.nusphere.com/contact_us

As of APC, I'm not sure how well it's maintained. I didn't notice any updates for long time and full support for php 5.3 appeared too late.